| GDAC_TopgenesforCluster1 expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/SKCM-TM/2399674/0.mRNAseq_preprocessor.Finished/SKCM-TM.uncv2.mRNAseq_RSEM_normalized_log2.txt |
| GDAC_TopgenesforCluster1 selectedgenes | 1500 |
| GDAC_NmfConsensusClustering2 k int | 2 |
| GDAC_NmfConsensusClustering2 k final | 10 |
| GDAC_CNMFselectcluster3 output | SKCM-TM |
| GDAC_CNMFselectcluster3 inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/SKCM-TM/2399674/0.mRNAseq_preprocessor.Finished/SKCM-TM.uncv2.mRNAseq_RSEM_normalized_log2.txt |
| GDAC_CnmfReports4 report | mRNAseq |
| Execution Times: | |
| Submitted: | 18:38:48 29-01-13 |
| Completed: | |
| Elapsed: | 01 hrs 56 mins 21 secs |
step 1. GDAC_TopgenesforCluster [id: 302389] This module can be used to selecte top genes with most variation, convert file to gct format, as well as imput missing value
urn:lsid:broadinstitute.org:cancer.genome.analysis:00205:35
| expfile | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/SKCM-TM/2399674/0.mRNAseq_preprocessor.Finished/SKCM-TM.uncv2.mRNAseq_RSEM_normalized_log2.txt |
| selectedgenes | 1500 |
| outputprefix | outputprefix |
| Output Files: | |
| .lsf.out | |
| outputprefix.expclu.gct | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 18:38:56 29-01-13 |
| Completed: | 18:53:13 29-01-13 |
| Elapsed: | 00 hrs 14 mins 16 secs |
step 2. GDAC_NmfConsensusClustering [id: 302390] Non-negative Matrix Factorization (NMF) Consensus Clustering, http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=89
urn:lsid:broadinstitute.org:cancer.genome.analysis:00379:39
| expfile | outputprefix.expclu.gct |
| k int | 2 |
| k final | 10 |
| outputprefix | cnmf |
| Execution Times: | |
| Submitted: | 18:38:56 29-01-13 |
| Completed: | 19:53:39 29-01-13 |
| Elapsed: | 01 hrs 14 mins 42 secs |
step 3. GDAC_CNMFselectcluster [id: 302391] selecte best cluster
urn:lsid:broadinstitute.org:cancer.genome.analysis:00226:39
| measure | Pearson |
| inputexp | outputprefix.expclu.gct |
| clumembership | cnmf.membership.txt |
| output | SKCM-TM |
| inputallexp | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/SKCM-TM/2399674/0.mRNAseq_preprocessor.Finished/SKCM-TM.uncv2.mRNAseq_RSEM_normalized_log2.txt |
| cophenetic | cnmf.cophenetic.coefficient.txt |
| Execution Times: | |
| Submitted: | 18:38:56 29-01-13 |
| Completed: | 20:32:45 29-01-13 |
| Elapsed: | 01 hrs 53 mins 48 secs |
step 4. GDAC_CnmfReports [id: 302392]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00414:22
| kclus | SKCM-TM.silfig.png |
| markers | SKCM-TM.subclassmarkers.txt |
| bestclu | SKCM-TM.bestclus.txt |
| allcluster | cnmf.membership.txt |
| cormatrix | SKCM-TM.cormatrix.png |
| file gif 2 | cnmf.consensus.plot.k2.png |
| file gif 3 | cnmf.consensus.plot.k3.png |
| file gif 4 | cnmf.consensus.plot.k4.png |
| file gif 5 | cnmf.consensus.plot.k5.png |
| file gif 6 | cnmf.consensus.plot.k6.png |
| file gif 7 | cnmf.consensus.plot.k7.png |
| file gif 8 | cnmf.consensus.plot.k8.png |
| expdata | outputprefix.expclu.gct |
| markersP | SKCM-TM.selectmarker.txt |
| heatmap | SKCM-TM.geneheatmap.png |
| heatmapall | SKCM-TM.geneheatmaptopgenes.png |
| report | mRNAseq |
| Output Files: | |
| nozzle.RData | |
| nozzle.html | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 18:38:56 29-01-13 |
| Completed: | 20:35:08 29-01-13 |
| Elapsed: | 01 hrs 56 mins 11 secs |
